The Gnotobiotics, Microbiology and Metagenomics Core (Core D), aims to identify the causal relationships between our colonizing microbiota and host health and disease, both in human clinical trials and in animal models. Core D supports more than 50 groups interested in evaluating mechanisms by which the host's microbiota affects health and disease, with particular focus to define functional effects of microbial communities in vivo. Our resources include an Intake Unit to handle logistics for sample and data collection, a Molecular Unit for sequence-based analyses, Microbiology Unit to analyze primary samples and manipulate isolates for functional studies, a Gnotobiotic (germfree) mouse facility for in vivo studies in animal models, and Computational Unit which includes bioinformatics and computational support, including access to computational clusters and personnel for assisting in experimental design and analysis of complex metagenomic datasets. As a core we provide support to nearly all academic centers in the greater Boston area.